OLUFF:一套新的发射型氧荧光素的基态和激发态力场参数。

IF 2.7 3区 化学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Photochemical & Photobiological Sciences Pub Date : 2024-11-13 DOI:10.1007/s43630-024-00654-y
Henar Mateo-delaFuente, Juan J Nogueira
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引用次数: 0

摘要

萤火虫生物发光系统的建模是了解氧荧光素/荧光素酶复合物的结合模式及其光物理特性的关键,其目的是开发高效的设备和技术。在这项工作中,我们提出了 OLUFF 力场,该力场能够描述四种可能的氧荧光素发光体在基态和激发态下的构象空间。我们对该力场进行了参数化,以再现量子力学(QM)能量和几何参数。此外,通过将基于 OLUFF 的分子动力学(MD)模拟获得的概率分布函数、最小化结构、红外光谱和法线模态分析与其量子力学对应物进行比较,对该力场进行了验证。此外,还使用通用琥珀力场(GAFF)进行了基态模拟,并与 OLUFF 进行了比较。结果表明,OLUFF 不仅很好地再现了 QM 特性,而且还改进了 GAFF 的结果。
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OLUFF: a novel set of ground and excited state force field parameters of the emitting oxyluciferin species.

The modeling of the bioluminescent system of fireflies is key to understand the binding mode of the oxyluciferin/luciferase complex and its photophysical properties with the aim of developing high-efficiency devices and techniques. In this work, we present the OLUFF force field, which is able to describe the interactions to sample the conformational space of the four possible oxyluciferin emitters in both ground and excited state. This force field has been parameterized to reproduce quantum mechanical (QM) energies and geometrical parameters. Moreover, it has been validated by comparing probability distribution functions, minimized structures, infrared spectra and normal mode analysis obtained from OLUFF-based molecular dynamic (MD) simulations with their QM counterparts. Additionally, ground state simulations have also been performed using the general amber force field (GAFF) and compared with the OLUFF. It has been demonstrated that the OLUFF not only reproduces well the QM properties, but also improves the results from the GAFF.

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来源期刊
Photochemical & Photobiological Sciences
Photochemical & Photobiological Sciences 生物-生化与分子生物学
CiteScore
5.60
自引率
6.50%
发文量
201
审稿时长
2.3 months
期刊介绍: A society-owned journal publishing high quality research on all aspects of photochemistry and photobiology.
期刊最新文献
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